========================================================================
 UT Genome Browser 1.0 RC1
                                                             2005.12.15
========================================================================

 UT Genome Browser

  UT Genome Browser ́CUCSC Genome Browser  Ensembl Genome Browser 
  悤 Web x[X̐QmuEUŁCȉ̂悤ȓ܂B

  * gbN͒PȂf[^ł͂ȂƗEFuAvP[Vł邽
    ߁C]̃QmuEUɂ͂Ȃ\͂Ɗgł܂B
  * gbŃCQmuEUɑ΂vOCIȋ@\񋟂ł܂B
    QmuEŨt[[N⃆[U[ GUI ɉłCƎ
    [Uɒ񋟂ł܂B
  * gbNƃt[[N̊Ԃ̒ʐM HTTP vgR XML 
    čs܂B
  * {IȃgbN͊ɒ񋟂Ă܂BႦ΁CQmz̈`q
    CGC% Ȃǂ̐ĺCɉł܂B
  * UT Genome Browser ƓĂgbN͎ PHP ŏĂ
    BCgbN錾ɓɐ͂܂B
  * UT Genome Browser ͏C BSD License ̂ƂŌJI[v\[X
    \tgEFAłB

 System requirements

  * Apache HTTP Server 1.3.x or Apache HTTP Server 2.0.x
  * PHP 4.4.x
  * PostgreSQL 7.4.x

 Installation

  UT Genome Browser  Fedora Core Linux  Cent OS Linux ł̓
  mFĂ܂BCXg[͈ȉ̎菇ōs܂B

  o PostgreSQL

  1. PostgreSQL ̃CXg[
     yum gł́Cȉ̃R}hŃCXg[ł܂B

       ------------------------------------------------------------------
       # yum install postgresql postgresql-server
       ------------------------------------------------------------------

  2. ANZX̕ύX
     /var/lib/pgsql/data/pg_hba.conf ȉ̂悤ɕύX܂B

       ------------------------------------------------------------------
       local all all trust
       host all all 127.0.0.1 255.255.255.255 trust
       host all all 192.168.0.0 255.255.255.0 trust
       ------------------------------------------------------------------

  3. TCP/IP ڑ̋
     /var/lib/pgsql/data ҏW tcpip_socket = true Ƃ܂B

  4. PostgreSQL ̋N
     PostgreSQL N܂BPostgreSQL  yum ŃCXg[ꍇC
     ȉ̃R}hŋNł܂B

       -------------------------------------------------
       # /etc/init.d/postgresql start
       -------------------------------------------------

  o PHP

  1. PHP ̃CXg[
     yum gł́Cȉ̃R}hŃCXg[ł܂B

       ------------------------------------------------------------------
       # yum install php php-pear
       ------------------------------------------------------------------

  2. t@CAbv[h̋
     /etc/php.ini ҏW file_uploads = On Ƃ܂B
     KvȂ upload_tmp_dir  upload_max_filesize KXύX܂B

  o UT Genome Browser

  1. install.pl ̕ҏW
     install.pl̈ȉ̕CXg[}V̊ɍ킹ĕύX
     ܂B

       # ύXĂ+++++++++++++++++++++++++++++++
       $PG_BIN="/usr/bin";
       $HTDOCS_PATH="/var/www";
       $BROWSER_URL="http://wwww.utgenome.org";
       $DB_HOST="localhost";
       $DBNAME_PREFIX="test";
       $DB_USER="browser";
       # +++++++++++++++++++++++++++++++++++++++++++++++++++++

     $PG_BIN         PostgreSQL ̎st@Cicreatedb, dropdb Ȃǁj
                     fBNg
     $HTDOC_PATH     UT Genome Browser CXg[fBNg
     $BROWSER_URL    UT Genome Browser CXg[fBNg
                     i$HTDOC_PATHj URL
     $DB_HOST        f[^x[X\z}ṼzXgB
     $DBNAME_PREFIX  PostgreSQL ̃f[^x[X̑Oɂ閼OB
     $DB_USER        UT Genome Browser p postgresql ̃[U

  2. CXg[̎s
     1. ŕҏW install.pl  root ňȉ̂悤Ɏs܂B

       -------------------------------------------------
       # perl install.pl
       -------------------------------------------------

     rɎ₪ꍇ́Cȉ̂悤ɉ񓚂܂B

       Shall the new user be allowed to create databases? (y/n) y
       Shall the new user be allowed to create more new users? (y/n) n

  3. f[^x[XփQmzf[^̑}
     install_data.plɂQmzf[^f[^x[X֊i[ł܂B
     zf[^fasta`ŗpӂĂB
     t@Cgenome.fastaƂ܂B

    Einstal_data.pl̈ȉ̕CXg[}V̊ɍ킹ĕύX܂B

       # ύXĂ+++++++++++++++++++++++++++++++
       $BROWSER_URL="http://www.utgenome.org";
       $DB_HOST="localhost";
       $DBNAME_PREFIX="test";
       $species="yeast";
       $revision="200407";
       $default_target="chr1";
       $default_start="1";
       $default_end="338304";
       $default_width="800";
       # +++++++++++++++++++++++++++++++++++++++++++++++++++++

     $BROWSER_URL    UT Genome Browser CXg[fBNg
                     i$HTDOC_PATHj URL
     $DB_HOST        f[^x[X\z}ṼzXgB
     $DBNAME_PREFIX  PostgreSQL ̃f[^x[X̑Oɂ閼OB

     install.plŎw肵̂Ɠ̂w肵܂B

     $species        Qmzf[^̎햼łB
     $revision       Qmzf[^̃rWłB
     $default_target ftHgŕ\^[QbgłB
     $default_start  ftHgŕ\^[Qbgz񒆂̊JnʒułB
     $default_end    ftHgŕ\^[Qbgz񒆂̏I~ʒułB
     $default_width  ftHgŃ^[Qbg\sNZłB

     Ef[^}̎s
     ---------------
     perl install_data.pl (fasta file)
     ---------------

     Ame[Vi[邷ꍇ́uVD`q̃L[[h\ɂ܂BvQƂĉB

  4. ApacheN܂B

     .htaccessLɂ邽߂ httpd.conf  ̈ȉ̕C܂B

     -----------------------------------------------------------------------------
     # This controls which options the .htaccess files in directories can
     # override. Can also be "All", or any combination of "Options", "FileInfo",
     # "AuthConfig", and "Limit"

     AllowOverride All   // NoneAllɏC

     # Controls who can get stuff from this server.
     -----------------------------------------------------------------------------

     ȉ̃R}hApacheN܂B
     -----------------------------------
     /etc/init.d/httpd start
     -----------------------------------

  5. uEUNĉ̊Ǘ҉ʂJǗ҂쐬܂B

     http://hogehoge.com/genome_browser/browser_manage_translate.php
    ihogehogeT[o[htdocsfBNg[genome_browserCXg[ꍇj

     ǗҖutestadminv/pX[huadminpasswdv̏ꍇA
     ȉ̂悤ɓ͂[Create New Administrator]{^܂B

     ------------------------------------
     [Administrator name]     testadmin
     [Password]               adminpasswd
     -------------------------------------

     ŃCXg[͊łB

  6. uEUNăQmuEUN܂B

     http://hogehoge.com/genome_browser/browser_keyword.php
    ihogehogeT[o[htdocsfBNg[genome_browserCXg[ꍇj


  7. `q̃L[[h\ɂ܂B(IvV)

     6. ܂łŔz񂻂̂̂{ł悤ɂȂ܂B
     ɂ́C̈`q݂ʒu\Ƃv܂B
     ̂߂Ɉ`qɂL[[hł悤ɂ܂B

     yeast ̏ꍇ͈`qQmzɃ}bsO

     ftp://ftp.yeastgenome.org/yeast/chromosomal_feature/saccharomyces_cerevisiae.gff

     擾܂B
     ȉ̃R}hskeywordsearchf[^x[Xɓo^܂B

     -------------------------------------------------------------------------------------------------------------------
     perl gff2keywordsearch_db_yeast.pl yeast 200407 < saccharomyces_cerevisiae.gff > saccharomyces_cerevisiae_kwd.sql
     psql -U postgres keywordsearch < saccharomyces_cerevisiae_kwd.sql
     -------------------------------------------------------------------------------------------------------------------

      sary pCfbNX̍\zs܂B
     ɂ͂܂L[[ḧꗗ kkkid (known key kind id) ɗ񋓂t@Cpӂ܂B
     ɂKeywordSearchf[^x[X ɑ΂Ĉȉ̂悤ȃR}h kkkid ̐s܂B

     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
     psql --no-align --command 'SELECT keyword FROM keyword WHERE kkkid=8;' --dbname keywordsearch --field-separator '' --tuples-only -U browser --output 'keyword_kid_where_kkkid_8.txt'
     psql --no-align --command 'SELECT keyword FROM keyword WHERE kkkid=9;' --dbname keywordsearch --field-separator '' --tuples-only -U browser --output 'keyword_kid_where_kkkid_9.txt'
     ...
     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

     ̃t@Cɑ΂mksary R}hŃCfbNX𐶐܂B

     --------------------------------------
     mksary keyword_kid_where_kkkid_8.txt
     mksary keyword_kid_where_kkkid_9.txt
     ...
     --------------------------------------

     쐬CfbNX̃pXȂǂ̏ browser_keyword_sary.php ňȉ̂悤Ɏw肵܂B
     ----------------------------------------------------------------------------------------------
     $browser_keyword_sary_path                        = '/usr/local/bin/sary';
     $browser_keyword_sary_index_directory             = '/home/utgb/browser_keyword_sary_index';
     $browser_keyword_sary_index_filename_prefix       = 'keyword_kid_where_kkkid_';
     $browser_keyword_sary_index_filename_suffix       = '.txt';
     $browser_keyword_sary_index_filename_index_suffix = '.txt.ary';
     ----------------------------------------------------------------------------------------------

     ŃL[[h\ɂȂ܂B
